malariagen_data.ag3.Ag3.cnv_hmm#

Ag3.cnv_hmm(region: str | Region | Mapping | List[str | Region | Mapping] | Tuple[str | Region | Mapping, ...], sample_sets: Sequence[str] | str | None = None, sample_query: str | None = None, max_coverage_variance: float | None = 0.2, inline_array: bool = True, chunks: str | Tuple[int, ...] = 'native') Dataset#

Access CNV HMM data from CNV calling.

Parameters#

regionstr or Region or Mapping or list of str or Region or Mapping or tuple of str or Region or Mapping

Region of the reference genome. Can be a contig name, region string (formatted like “{contig}:{start}-{end}”), or identifier of a genome feature such as a gene or transcript. Can also be a sequence (e.g., list) of regions.

sample_setssequence of str or str or None, optional

List of sample sets and/or releases. Can also be a single sample set or release.

sample_querystr or None, optional

A pandas query string to be evaluated against the sample metadata, to select samples to be included in the returned data.

max_coverage_variancefloat or None, optional, default: 0.2

Remove samples if coverage variance exceeds this value.

inline_arraybool, optional, default: True

Passed through to dask from_array().

chunksstr or tuple of int, optional, default: ‘native’

If ‘auto’ let dask decide chunk size. If ‘native’ use native zarr chunks. Also, can be a target size, e.g., ‘200 MiB’, or a tuple of integers.

Returns#

Dataset

An xarray dataset of CNV HMM calls and associated data.